{
  "data": {
    "BrainMask": "",
    "CerebellumMask": "",
    "T1img": "/data/proj/app/img/Owl_Oriented/100604-200_1_OwlOrient.nii.gz",
    "T2img": "",
    "TissueSeg": "",
    "SubjectVentricleMask": "",
    "output_dir": "/data/proj/app/pipeline/eacsf/Outputs_15Aug2019"
  },
  "parameters": {
    "ACPC_index": 70,
    "ACPC_mm": 0,
    "ANTS_T1_weight": 1,
    "ANTS_gaussian_sig": 3,
    "ANTS_iterations_val": "100x50x25",
    "ANTS_reg_type": "GreedyDiffeo",
    "ANTS_sim_metric": "CC",
    "ANTS_sim_param": 4,
    "ANTS_transformation_step": 0.25,
    "templateT1Ventricle": "/data/proj/app/pipeline/eacsf/Atlases/TissueSegmentation_Atlases/DeepGray5Class_stripped/template.nrrd",
    "templateInvMaskVentricle": "/data/proj/app/pipeline/eacsf/Atlases/TissueSegmentation_Atlases/DeepGray5Class_stripped/Vent_CSF-INVMask.nrrd",
    "registrationAtlas": "/data/proj/app/pipeline/eacsf/Atlases/TissueSegmentation_Atlases/1year-Average-IBIS-MNI-t1w.nrrd",
    "skullStrippingAtlasesDirectory": "/data/proj/app/pipeline/eacsf/Atlases/SkullStripping_Atlases/",
    "tissueSegAtlasDirectory": "/data/proj/app/pipeline/eacsf/Atlases/TissueSegmentation_Atlases/DeepGray5Class_stripped",
    "CSFLabel": 3,
    "LH_innerSurface": "",
    "RH_innerSurface": ""
  },
  "executables": [
    {
      "name": "ABC_CLI",
      "path": "/data/proj/app/pipeline/eacsf/code/AutoEACSF_v1.4/Auto_EACSF-release-v1.4/usr/bin/"
    },
    {
      "name": "ANTS",
      "path": "/data/proj/app/pipeline/eacsf/code/AutoEACSF_v1.4/Auto_EACSF-release-v1.4/usr/bin/"
    },
    {
      "name": "BRAINSFit",
      "path": "/data/proj/app/pipeline/eacsf/code/AutoEACSF_v1.4/Auto_EACSF-release-v1.4/usr/bin/"
    },
    {
      "name": "ImageMath",
      "path": "/data/proj/app/pipeline/eacsf/code/AutoEACSF_v1.4/Auto_EACSF-release-v1.4/usr/bin/"
    },
    {
      "name": "ImageStat",
      "path": "/data/proj/app/pipeline/eacsf/code/AutoEACSF_v1.4/Auto_EACSF-release-v1.4/usr/bin/"
    },
    {
      "name": "WarpImageMultiTransform",
      "path": "/data/proj/app/pipeline/eacsf/code/AutoEACSF_v1.4/Auto_EACSF-release-v1.4/usr/bin/"
    },
    {
      "name": "bet",
      "path": ""
    },
    {
      "name": "convertITKformats",
      "path": "/data/proj/app/pipeline/eacsf/code/AutoEACSF_v1.4/Auto_EACSF-release-v1.4/usr/bin/"
    },
    {
      "name": "python3",
      "path": ""
    }
  ],
  "scripts": [
    {
      "name": "main_script",
      "executables": [
        "python3",
        "ImageMath",
        "ImageStat",
        "ABC_CLI"
      ]
    },
    {
      "name": "rigid_align",
      "executables": [
        "BRAINSFit"
      ]
    },
    {
      "name": "make_mask",
      "executables": [
        "ImageMath",
        "bet",
        "convertITKformats",
        "ANTS",
        "WarpImageMultiTransform"
      ]
    },
    {
      "name": "tissue_seg",
      "executables": [
        "BRAINSFit",
        "ANTS",
        "WarpImageMultiTransform",
        "ABC_CLI"
      ]
    },
    {
      "name": "vent_mask",
      "executables": [
        "ImageMath",
        "ANTS",
        "WarpImageMultiTransform"
      ]
    }
  ]
}